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Paoletti F, Covaceuszach S, Cassetta A, Calabrese AN, Novak U, Konarev P, Grdadolnik J, Lamba D, Golič Grdadolnik S. Distinct conformational changes occur within the intrinsically unstructured pro-domain of pro-Nerve Growth Factor in the presence of ATP and Mg 2. Protein Sci 2023; 32:e4563. [PMID: 36605018 PMCID: PMC9878617 DOI: 10.1002/pro.4563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/24/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023]
Abstract
Nerve growth factor (NGF), the prototypical neurotrophic factor, is involved in the maintenance and growth of specific neuronal populations, whereas its precursor, proNGF, is involved in neuronal apoptosis. Binding of NGF or proNGF to TrkA, p75NTR , and VP10p receptors triggers complex intracellular signaling pathways that can be modulated by endogenous small-molecule ligands. Here, we show by isothermal titration calorimetry and NMR that ATP binds to the intrinsically disordered pro-peptide of proNGF with a micromolar dissociation constant. We demonstrate that Mg2+ , known to play a physiological role in neurons, modulates the ATP/proNGF interaction. An integrative structural biophysics analysis by small angle X-ray scattering and hydrogen-deuterium exchange mass spectrometry unveils that ATP binding induces a conformational rearrangement of the flexible pro-peptide domain of proNGF. This suggests that ATP may act as an allosteric modulator of the overall proNGF conformation, whose likely distinct biological activity may ultimately affect its physiological homeostasis.
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Affiliation(s)
- Francesca Paoletti
- Laboratory for Molecular Structural Dynamics, Theory DepartmentNational Institute of ChemistryLjubljanaSlovenia
| | | | - Alberto Cassetta
- Institute of Crystallography—C.N.R.—Trieste OutstationTriesteItaly
| | - Antonio N. Calabrese
- School of Molecular and Cellular Biology, Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
| | - Urban Novak
- Laboratory for Molecular Structural Dynamics, Theory DepartmentNational Institute of ChemistryLjubljanaSlovenia
| | - Petr Konarev
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics”Russian Academy of SciencesMoscowRussia
| | - Jože Grdadolnik
- Laboratory for Molecular Structural Dynamics, Theory DepartmentNational Institute of ChemistryLjubljanaSlovenia
| | - Doriano Lamba
- Institute of Crystallography—C.N.R.—Trieste OutstationTriesteItaly
- Interuniversity Consortium “Biostructures and Biosystems National Institute”RomeItaly
| | - Simona Golič Grdadolnik
- Laboratory for Molecular Structural Dynamics, Theory DepartmentNational Institute of ChemistryLjubljanaSlovenia
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2
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Paoletti F, Merzel F, Cassetta A, Ogris I, Covaceuszach S, Grdadolnik J, Lamba D, Golič Grdadolnik S. Endogenous modulators of neurotrophin signaling: Landscape of the transient ATP-NGF interactions. Comput Struct Biotechnol J 2021; 19:2938-2949. [PMID: 34136093 PMCID: PMC8164016 DOI: 10.1016/j.csbj.2021.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/29/2021] [Accepted: 05/02/2021] [Indexed: 12/02/2022] Open
Abstract
High-resolution solution NMR structure of rhNGF has been determined. Quinary interactions characterize ATP binding to rhNGF. SPR, ITC and STD-NMR reveal ATP binding to rhNGF with mM affinity. NMR and MD analysis pinpoint to the presence of two binding sites of ATP on rhNGF. Stoichiometry of ATP-Mg2+ or Zn2+-rhNGF mixtures affects KD affinity to TrkA/p75NTR.
The Nerve Growth Factor (NGF) neurotrophin acts in the maintenance and growth of neuronal populations. Despite the detailed knowledge of NGF’s role in neuron physiology, the structural and mechanistic determinants of NGF bioactivity modulated by essential endogenous ligands are still lacking. We present the results of an integrated structural and advanced computational approach to characterize the extracellular ATP-NGF interaction. We mapped by NMR the interacting surface and ATP orientation on NGF and revealed the functional role of this interaction in the binding to TrkA and p75NTR receptors by SPR. The role of divalent ions was explored in conjunction with ATP. Our results pinpoint ATP as a likely transient molecular modulator of NGF signaling, in health and disease states.
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Key Words
- ARIA, Ambiguous Restraints for Iterative Assignment
- ATP modulation
- BDNF, Brain Derived Neurotrophic Factor
- CARA, Computer Aided Resonance Assignment
- CS-E, Chrondroitin Sulfate E
- CSP, Chemical Shift Perturbation
- DSF, Differential Scanning Fluorimetry
- EI-MS, Electron Ionization Mass Spectrometry
- Endogenous ligands
- FGF2, Fibroblast Growth Factor 2
- FT-IR, Fourier Transform Infrared Spectroscopy
- HBD, Heparin Binding Domain
- HSQC, Heteronuclear Single Quantum Coherence
- ITC, Isothermal Titration Calorimetry
- MALDI-TOF MS, Matrix Assisted Laser Desorption Ionization-Time Of Flight Mass Spectrometry
- MD, Molecular Dynamics
- MS, Mass Spectrometry
- NGF interactions
- NGF, Nerve Growth Factor
- NMR, Nuclear Magnetic Resonance
- NOE, Nuclear Overhouser Effect
- NOESY, Nuclear Overhauser Effect Spectroscopy
- NT, NeuroTrophin
- Neurotrophins
- P20, Polysorbate 20
- PME, Particle Mesh Ewald
- RMSD, Root Mean Square Deviation
- SAR, Structure-Activity Relationship
- SPR, Surface Plasmon Resonance
- STD, Saturation-Transfer Difference
- TrkA, Tyrosine Kinase Receptor A
- TrkA, p75NTR receptors
- p75NTR, p75 NeuroTrophin Receptor
- proNGF, proNGF – NGF precursor
- rh-proNGF, recombinant human proNGF – NGF precursor
- rhNGF, recombinant human NGF
- rmNGF, recombinant mouse NGF
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Affiliation(s)
- Francesca Paoletti
- Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Franci Merzel
- Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Alberto Cassetta
- Institute of Crystallography - C.N.R.- Trieste Outstation. Area Science Park - Basovizza, S.S.14 - Km. 163.5, I-34149 Trieste, Italy
| | - Iza Ogris
- Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Sonia Covaceuszach
- Institute of Crystallography - C.N.R.- Trieste Outstation. Area Science Park - Basovizza, S.S.14 - Km. 163.5, I-34149 Trieste, Italy
| | - Jože Grdadolnik
- Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Doriano Lamba
- Institute of Crystallography - C.N.R.- Trieste Outstation. Area Science Park - Basovizza, S.S.14 - Km. 163.5, I-34149 Trieste, Italy.,Interuniversity Consortium "Biostructures and Biosystems National Institute", Viale delle Medaglie d'Oro 305, I-00136 Roma, Italy
| | - Simona Golič Grdadolnik
- Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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3
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Ogris I, Zelenko U, Sosič I, Gobec M, Skubic C, Ivanov M, Soković M, Kocjan D, Rozman D, Golič Grdadolnik S. Pyridylethanol(phenylethyl)amines are non-azole, highly selective Candida albicans sterol 14α-demethylase inhibitors. Bioorg Chem 2020; 106:104472. [PMID: 33261849 DOI: 10.1016/j.bioorg.2020.104472] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/10/2020] [Indexed: 12/17/2022]
Abstract
Sterol 14α-demethylase (CYP51) is the main drug target for the treatment of fungal infections. The worldwide increase in the incidence of opportunistic fungal infections and the emerging resistance to available azole-based antifungal drugs, raise the need to develop structurally distinct and selective fungal CYP51 inhibitors. In this work we have, for the first time, investigated the binding of pyridylethanol(phenylethyl)amines to any fungal CYP51. The comparison of the binding to Candida albicans and human CYP51 studied by spectroscopic and modeling methods revealed moieties decisive for selectivity and potency and resulted in the development of highly selective derivatives with significantly increased inhibitory potency. The structure-based insight into the selectivity requirements of this new chemical class of fungal CYP51 inhibitors, their unique binding properties and the low molecular weight of lead derivatives offer novel directions for the targeted development of antifungal clinical candidates.
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Affiliation(s)
- Iza Ogris
- Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
| | - Urška Zelenko
- Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Martina Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Cene Skubic
- Center for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Marija Ivanov
- Institute for Biological Research "Siniša Stanković"- National Institute of Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia
| | - Marina Soković
- Institute for Biological Research "Siniša Stanković"- National Institute of Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia
| | - Darko Kocjan
- Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
| | - Damjana Rozman
- Center for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Simona Golič Grdadolnik
- Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia.
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Jeong H, Lee JJ, Lee J, Na K. A Multiligand Architectural Photosensitizer That Targets Hemagglutinin on Envelope of Influenza Virus for Photodynamic Inactivation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2000556. [PMID: 32329578 DOI: 10.1002/smll.202000556] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/25/2020] [Accepted: 04/06/2020] [Indexed: 05/22/2023]
Abstract
The efficacy of current antiviral drugs used to treat influenza has been declining because of mutations and resistance of the virus. Herein, a light-sensitive multiligand architecture is developed consisting of chitosan conjugated to a photosensitizer and 6'-sialyllactose (SL) to develop an antiviral agent against influenza with a different mechanism of action (SL-chitosan-Chlorin e6, SCC). Saturation transfer difference-nuclear magnetic resonance determined that the ability of SCC to bind to viral hemagglutinin is stronger than that of the monomeric substance. Virus recognition is confirmed by immunofluorescence and transmission electron microscope imaging. SCC induces viral inactivation by causing permanent membrane damage through its photoactivity. Viral membrane is oxidized by the photoactivity of SCC, thus, the virus membrane collapses. Furthermore, using the plaque reduction assay to evaluate the inhibitory effect of SCC on influenza A and B, it is found that its antiviral effects are 23% and 50% higher than the conventional antiviral drug. Additionally, SCC prevents infection by influenza in 100% of mice subjected to laser irradiation. These results indicate that this photodynamic multiligand structure can overcome the limitations of existing antiviral agents and suggest a pertinent methodology of prophylaxis and treatment by preemptively attacking the virus before it enters the host cell.
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Affiliation(s)
- Hayoon Jeong
- Department of Biotechnology, The Catholic University of Korea, 43 Jibong-ro, Wonmi-gu, Bucheon-si, Gyeonggi-do, 14662, Korea
- Department of Biomedical-Chemical Engineering, The Catholic University of Korea, 43 Jibong-ro, Wonmi-gu, Bucheon-si, Gyeonggi-do, 14662, Korea
| | - Jeong-Ju Lee
- Department of Biotechnology, The Catholic University of Korea, 43 Jibong-ro, Wonmi-gu, Bucheon-si, Gyeonggi-do, 14662, Korea
| | - Jangsu Lee
- Department of Biotechnology, The Catholic University of Korea, 43 Jibong-ro, Wonmi-gu, Bucheon-si, Gyeonggi-do, 14662, Korea
- Department of Biomedical-Chemical Engineering, The Catholic University of Korea, 43 Jibong-ro, Wonmi-gu, Bucheon-si, Gyeonggi-do, 14662, Korea
| | - Kun Na
- Department of Biotechnology, The Catholic University of Korea, 43 Jibong-ro, Wonmi-gu, Bucheon-si, Gyeonggi-do, 14662, Korea
- Department of Biomedical-Chemical Engineering, The Catholic University of Korea, 43 Jibong-ro, Wonmi-gu, Bucheon-si, Gyeonggi-do, 14662, Korea
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5
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Direct visualization of avian influenza H5N1 hemagglutinin precursor and its conformational change by high-speed atomic force microscopy. Biochim Biophys Acta Gen Subj 2020; 1864:129313. [DOI: 10.1016/j.bbagen.2019.02.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/19/2019] [Accepted: 02/26/2019] [Indexed: 01/06/2023]
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6
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Arenas AF, Arango-Plaza N, Arenas JC, Salcedo GE. Time-Frequency Approach Applied to Finding Interaction Regions in Pathogenic Proteins. Bioinform Biol Insights 2019; 13:1177932219850172. [PMID: 31210729 PMCID: PMC6552352 DOI: 10.1177/1177932219850172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 04/18/2019] [Indexed: 11/15/2022] Open
Abstract
Protein-protein interactions govern all molecular processes for living organisms, even those involved in pathogen infection. Pathogens such as virus, bacteria, and parasites contain proteins that help the pathogen to attach, penetrate, and settle inside the target cell. Thus, it is necessary to know the regions in pathogenic proteins that interact with host cell receptors. Currently, powerful pathogen databases are available and many pathogenic proteins have been recognized, but many pathogenic proteins have not been characterized. This work developed a program in MATLAB environment based on the time-frequency analysis to recognize important sites in proteins. Our program highlights the highest energy patches in proteins from their time-frequency distribution and matches the corresponding frequency. We sought to know if this approach is able to recognize stretches residues related to interaction. Our approach was applied to five study cases from pathogenic co-crystallized structures that have been well characterized. We searched the frequencies that characterize interaction regions in pathogenic proteins and with this information tried to identify new interaction patches in either paralogs or orthologs. We found that our program generates a well-interpretable graphic under several descriptors that can show important regions in proteins even those related to interaction. We propose that this MATLAB program could be used as a tool to explore outstanding regions in uncharacterized proteins.
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Affiliation(s)
- Ailan F Arenas
- Grupo de Estudio en Parasitología Molecular (Gepamol), Universidad del Quindío, Armenia, Colombia.,Grupo de Investigación y Asesoría en Estadística, Universidad del Quindío, Armenia, Colombia
| | - Nicolás Arango-Plaza
- Grupo de Investigación y Asesoría en Estadística, Universidad del Quindío, Armenia, Colombia
| | - Juan Camilo Arenas
- Grupo de Estudio en Parasitología Molecular (Gepamol), Universidad del Quindío, Armenia, Colombia.,Grupo de Investigación y Asesoría en Estadística, Universidad del Quindío, Armenia, Colombia
| | - Gladys E Salcedo
- Grupo de Investigación y Asesoría en Estadística, Universidad del Quindío, Armenia, Colombia
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7
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Reiter-Scherer V, Cuellar-Camacho JL, Bhatia S, Haag R, Herrmann A, Lauster D, Rabe JP. Force Spectroscopy Shows Dynamic Binding of Influenza Hemagglutinin and Neuraminidase to Sialic Acid. Biophys J 2019; 116:1037-1048. [PMID: 30799074 DOI: 10.1016/j.bpj.2019.01.041] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/30/2018] [Accepted: 01/14/2019] [Indexed: 10/27/2022] Open
Abstract
The influenza A virus infects target cells through multivalent interactions of its major spike proteins, hemagglutinin (HA) and neuraminidase (NA), with the cellular receptor sialic acid (SA). HA is known to mediate the attachment of the virion to the cell, whereas NA enables the release of newly formed virions by cleaving SA from the cell. Because both proteins target the same receptor but have antagonistic functions, virus infection depends on a properly tuned balance of the kinetics of HA and NA activities for viral entry to and release from the host cell. Here, dynamic single-molecule force spectroscopy, based on scanning force microscopy, was employed to determine these bond-specific kinetics, characterized by the off rate koff, rupture length xβ and on rate kon, as well as the related free-energy barrier ΔG and the dissociation constant KD. Measurements were conducted using surface-immobilized HA and NA of the influenza A virus strain A/California/04/2009 and a novel, to our knowledge, synthetic SA-displaying receptor for functionalization of the force probe. Single-molecule force spectroscopy at force loading rates between 100 and 50,000 pN/s revealed most probable rupture forces of the protein-SA bond in the range of 10-100 pN. Using an extension of the widely applied Bell-Evans formalism by Friddle, De Yoreo, and co-workers, it is shown that HA features a smaller xβ, a larger koff and a smaller ΔG than NA. Measurements of the binding probability at increasing contact time between the scanning force microscopy force probe and the surface allow an estimation of KD, which is found to be three times as large for HA than for NA. This suggests a stronger interaction for NA-SA than for HA-SA. The biological implications in regard to virus binding to the host cell and the release of new virions from the host cell are discussed.
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Affiliation(s)
| | | | - Sumati Bhatia
- Department of Chemistry, Freie Universität Berlin, Berlin, Germany
| | - Rainer Haag
- Department of Chemistry, Freie Universität Berlin, Berlin, Germany
| | - Andreas Herrmann
- Department of Biology and IRI Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Daniel Lauster
- Department of Biology and IRI Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Jürgen P Rabe
- Department of Physics and IRIS Adlershof, Humboldt-Universität zu Berlin, Berlin, Germany.
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8
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Unravelling the Role of O-glycans in Influenza A Virus Infection. Sci Rep 2018; 8:16382. [PMID: 30401951 PMCID: PMC6219607 DOI: 10.1038/s41598-018-34175-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 10/09/2018] [Indexed: 11/09/2022] Open
Abstract
The initial stage of host cell infection by influenza A viruses (IAV) is mediated through interaction of the viral haemagglutinin (HA) with cell surface glycans. The binding requirement of IAVs for Galβ(1,4)Glc/ GlcNAc (lactose/lactosamine) glycans with a terminal α(2,6)-linked (human receptors) or α(2,3)-linked (avian receptors) N-acetylneuraminic residue commonly found on N-glycans, is well-established. However the role and significance of sialylated Galβ(1,3)GalNAc (core 1) epitopes that are typical O-glycoforms in influenza virus pathogenesis remains poorly detailed. Here we report a multidisciplinary study using NMR spectroscopy, virus neutralization assays and molecular modelling, into the potential for IAV to engage sialyl-Galβ(1,3)GalNAc O-glycoforms for cell attachment. H5 containing virus like particles (VLPs) derived from an H5N1 avian IAV strain show a significant involvement of the O-glycan-specific GalNAc residue, coordinated by a EQTKLY motif conserved in highly pathogenic avian influenza (HPAI) strains. Notably, human pandemic H1N1 influenza viruses shift the preference from 'human-like' α(2,6)-linkages in sialylated Galβ(1,4)Glc/GlcNAc fragments to 'avian-like' α(2,3)-linkages in sialylated Galβ(1,3)GalNAc without involvement of the GalNAc residue. Overall, our study suggests that sialylated Galβ(1,3)GalNAc as O-glycan core 1 glycoforms are involved in the influenza A virus life cycle and play a particularly crucial role during infection of HPAI strains.
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9
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Anti-Influenza A Viral Butenolide from Streptomyces sp. Smu03 Inhabiting the Intestine of Elephas maximus. Viruses 2018; 10:v10070356. [PMID: 29976861 PMCID: PMC6070878 DOI: 10.3390/v10070356] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 06/25/2018] [Accepted: 06/26/2018] [Indexed: 12/25/2022] Open
Abstract
Actinobacteria are a phylum of bacteria known for their potential in producing structurally diversified natural products that are always associated with a broad range of biological activities. In this paper, using an H5N1 pseudo-typed virus drug screening system combined with a bioassay guided purification approach, an antiviral butanolide (1) was identified from the culture broth of Streptomyces sp. SMU03, a bacterium isolated from the feces of Elephas maximus in Yunnan province, China. This compound displayed broad and potent activity against a panel of influenza viruses including H1N1 and H3N2 subtypes, as well as influenza B virus and clinical isolates with half maximal inhibitory concentration values (IC50) in the range of 0.29 to 12 µg/mL. In addition, 1 was also active against oseltamivir-resistant influenza virus strain of A/PR/8/34 with NA-H274Y mutation. Studies on the detailed modes of action suggested that 1 functioned by interfering with the fusogenic process of hemagglutinin (HA) of influenza A virus (IAV), thereby blocking the entry of virus into host cells. Furthermore, the anti-IAV activity of 1 was assessed with infected BALB/c mice, of which the appearance, weight, and histopathological changes in the infected lungs were significantly alleviated compared with the no-drug-treated group. Conclusively, these results provide evidence that natural products derived from microbes residing in animal intestines might be a good source for antiviral drug discovery.
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10
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Leiva R, Barniol-Xicota M, Codony S, Ginex T, Vanderlinden E, Montes M, Caffrey M, Luque FJ, Naesens L, Vázquez S. Aniline-Based Inhibitors of Influenza H1N1 Virus Acting on Hemagglutinin-Mediated Fusion. J Med Chem 2017; 61:98-118. [PMID: 29220568 DOI: 10.1021/acs.jmedchem.7b00908] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Two series of easily accessible anilines were identified as inhibitors of influenza A virus subtype H1N1, and extensive chemical synthesis and analysis of the structure-activity relationship were performed. The compounds were shown to interfere with low pH-induced membrane fusion mediated by the H1 and H5 (group 1) hemagglutinin (HA) subtypes. A combination of virus resistance, HA interaction, and molecular dynamics simulation studies elucidated the binding site of these aniline-based influenza fusion inhibitors, which significantly overlaps with the pocket occupied by some H3 HA-specific inhibitors, indicating the high relevance of this cavity for drug design.
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Affiliation(s)
- Rosana Leiva
- Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona , Av. Joan XXIII, 27-31, Barcelona E-08028, Spain
| | - Marta Barniol-Xicota
- Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona , Av. Joan XXIII, 27-31, Barcelona E-08028, Spain
| | - Sandra Codony
- Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona , Av. Joan XXIII, 27-31, Barcelona E-08028, Spain
| | - Tiziana Ginex
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), Universitat de Barcelona , Av. Prat de la Riba 171, Santa Coloma de Gramanet E-08921, Spain
| | | | - Marta Montes
- Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona , Av. Joan XXIII, 27-31, Barcelona E-08028, Spain
| | - Michael Caffrey
- Department of Biochemistry & Molecular Genetics, University of Illinois at Chicago , 900 South Ashland Avenue, Chicago, Illinois 60607, United States
| | - F Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), Universitat de Barcelona , Av. Prat de la Riba 171, Santa Coloma de Gramanet E-08921, Spain
| | - Lieve Naesens
- Rega Institute for Medical Research, KU Leuven , B-3000 Leuven, Belgium
| | - Santiago Vázquez
- Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona , Av. Joan XXIII, 27-31, Barcelona E-08028, Spain
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11
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Kingsley CN, Antanasijevic A, Palka-Hamblin H, Durst M, Ramirez B, Lavie A, Caffrey M. Probing the metastable state of influenza hemagglutinin. J Biol Chem 2017; 292:21590-21597. [PMID: 29127198 DOI: 10.1074/jbc.m117.815043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/05/2017] [Indexed: 12/24/2022] Open
Abstract
Viral entry into host cells is mediated by membrane proteins in a metastable state that transition to a more stable state upon a stimulus. For example, in the influenza envelope protein hemagglutinin (HA), the low pH in the endosome triggers a transition from the metastable prefusion conformation to the stable fusion conformation. To identify probes that interfere with HA function, here we screened a library of H7 HA peptides for inhibition of H7 HA-mediated entry. We discovered a peptide, PEP87 (WSYNAELLVAMENQHTI), that inhibited H7 and H5 HA-mediated entry. PEP87 corresponds to a highly conserved helical region of the HA2 subunit of HA that self-interacts in the neutral pH conformation. Mutagenesis experiments indicated that PEP87 binds to its native region in the HA trimer. We also found that PEP87 is unstructured in isolation but tends to form a helix as evidenced by CD and NMR studies. Fluorescence, chemical cross-linking, and saturation transfer difference NMR data suggested that PEP87 binds to the neutral pH conformation of HA and disrupts the HA structure without affecting its oligomerization state. Together, this work provides support for a model in which PEP87 disrupts HA function by displacing native interactions of the neutral pH conformation. Moreover, our observations indicate that the HA prefusion structure (and perhaps the metastable states of other viral entry proteins) is more dynamic with transient motions being larger than generally appreciated. These findings also suggest that the ensemble of prefusion structures presents many potential sites for targeting in therapeutic interventions.
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Affiliation(s)
- Carolyn N Kingsley
- From the Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois 60607
| | - Aleksandar Antanasijevic
- From the Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois 60607
| | - Helena Palka-Hamblin
- From the Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois 60607
| | - Matthew Durst
- From the Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois 60607
| | - Benjamin Ramirez
- From the Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois 60607
| | - Arnon Lavie
- From the Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois 60607
| | - Michael Caffrey
- From the Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois 60607
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12
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Aizpurua-Olaizola O, Sastre Torano J, Pukin A, Fu O, Boons GJ, de Jong GJ, Pieters RJ. Affinity capillary electrophoresis for the assessment of binding affinity of carbohydrate-based cholera toxin inhibitors. Electrophoresis 2017; 39:344-347. [DOI: 10.1002/elps.201700207] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 08/25/2017] [Accepted: 09/07/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Oier Aizpurua-Olaizola
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences; Utrecht University; Utrecht Netherlands
| | - Javier Sastre Torano
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences; Utrecht University; Utrecht Netherlands
| | - Aliaksei Pukin
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences; Utrecht University; Utrecht Netherlands
| | - Ou Fu
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences; Utrecht University; Utrecht Netherlands
| | - Geert Jan Boons
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences; Utrecht University; Utrecht Netherlands
| | - Gerhardus J. de Jong
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences; Utrecht University; Utrecht Netherlands
| | - Roland J. Pieters
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences; Utrecht University; Utrecht Netherlands
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13
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Shelby T, Banerjee T, Kallu J, Sulthana S, Zegar I, Santra S. Novel magnetic relaxation nanosensors: an unparalleled "spin" on influenza diagnosis. NANOSCALE 2016; 8:19605-19613. [PMID: 27778002 DOI: 10.1039/c6nr05889b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Rapid detection and diagnosis of pathogenic strains of influenza is necessary for expedited treatment and quicker resolutions to the ever-rising flu pandemics. Considering this, we propose the development of novel magnetic relaxation nanosensors (MRnS) for the rapid detection of influenza through targeted binding with hemagglutinin. 2,6- and 2,3-sialic acid ligands and entry blocker peptides are conjugated to iron oxide nanoparticles to create functional MRnS. Positive detection of various hemagglutinin variants (H1 and H5) is possible with protein concentrations as little as 1.0 nM. Most importantly, detection using functional MRnS is achieved within minutes and differentiates between influenza subtypes. This specificity allows mixtures of MRnS to screen for multiple pathogens at once, discarding the need to conduct multiple individual tests. Current methods used to diagnose influenza, such as RT-PCR and viral culturing, while largely effective, are complex, time-consuming and costly. As well, they are not as sensitive or specific, and have been known to produce false-positive results. In contrast to these methods, targeted MRnS are robust, point-of-care diagnostic tools featuring simple, rapid and low-cost procedures. These qualities, as well as high sensitivity and specificity, and low turnaround times, make a strong case for the diagnostic application of MRnS in clinical settings.
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Affiliation(s)
- Tyler Shelby
- Department of Chemistry and KPRC, Pittsburg State University, 1701 S. Broadway Street, Pittsburg, KS 66762, USA.
| | - Tuhina Banerjee
- Department of Chemistry and KPRC, Pittsburg State University, 1701 S. Broadway Street, Pittsburg, KS 66762, USA.
| | - Jyothi Kallu
- Department of Chemistry and KPRC, Pittsburg State University, 1701 S. Broadway Street, Pittsburg, KS 66762, USA.
| | - Shoukath Sulthana
- Department of Chemistry and KPRC, Pittsburg State University, 1701 S. Broadway Street, Pittsburg, KS 66762, USA.
| | - Irene Zegar
- Department of Chemistry and KPRC, Pittsburg State University, 1701 S. Broadway Street, Pittsburg, KS 66762, USA.
| | - Santimukul Santra
- Department of Chemistry and KPRC, Pittsburg State University, 1701 S. Broadway Street, Pittsburg, KS 66762, USA.
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14
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Antanasijevic A, Hafeman NJ, Tundup S, Kingsley C, Mishra RK, Rong L, Manicassamy B, Wardrop D, Caffrey M. Stabilization and Improvement of a Promising Influenza Antiviral: Making a PAIN PAINless. ACS Infect Dis 2016; 2:608-615. [PMID: 27759373 DOI: 10.1021/acsinfecdis.6b00046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The viral envelope protein hemagglutinin (HA) plays a critical role in influenza entry and thus is an attractive target for novel therapeutics. The small molecule tert-butylhydroquinone (TBHQ) has previously been shown to bind to HA and inhibit HA-mediated entry with low micromolar potency. However, enthusiasm for the use of TBHQ has diminished due to the compound's antioxidant properties. In this work we show that the antioxidant properties of TBHQ are not responsible for the inhibition of HA-mediated entry. In addition, we have performed a structure-activity relationship (SAR) analysis of TBHQ derivatives. We find that the most promising compound, 3-tert-butyl-4-methoxyphenol, exhibits enhanced potency (IC50 = 0.6 μM), decreased toxicity (CC50 = 340 μM), and increased stability (t1/2 > 48 h). Finally, we have characterized the binding properties of 3-tert-butyl-4-methoxyphenol using NMR and molecular dynamics to guide future efforts for chemical optimization.
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Affiliation(s)
- Aleksandar Antanasijevic
- Department of Biochemistry & Molecular Genetics, University of Illinois at Chicago, 900 South Ashland Avenue, Chicago, Illinois 60607, United States
| | - Nicholas J. Hafeman
- Department
of Chemistry, University of Illinois at Chicago, 845 West Taylor
Street, Chicago, Illinois 60607, United States
| | - Smanla Tundup
- Department
of Microbiology and Immunology, University of Chicago, 920 East
58th Street, Chicago, Illinois 60637, United States
| | - Carolyn Kingsley
- Department of Biochemistry & Molecular Genetics, University of Illinois at Chicago, 900 South Ashland Avenue, Chicago, Illinois 60607, United States
| | - Rama K. Mishra
- Center for Molecular Innovation and Drug Discovery, Northwestern University, 2135 Sheridan Road, Evanston, Illinois 60208, United States
| | - Lijun Rong
- Department of Microbiology & Immunology, University of Illinois at Chicago, 835 South Wolcott, Chicago, Illinois 60612, United States
| | - Balaji Manicassamy
- Department
of Microbiology and Immunology, University of Chicago, 920 East
58th Street, Chicago, Illinois 60637, United States
| | - Duncan Wardrop
- Department
of Chemistry, University of Illinois at Chicago, 845 West Taylor
Street, Chicago, Illinois 60607, United States
| | - Michael Caffrey
- Department of Biochemistry & Molecular Genetics, University of Illinois at Chicago, 900 South Ashland Avenue, Chicago, Illinois 60607, United States
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15
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Marchetti R, Perez S, Arda A, Imberty A, Jimenez‐Barbero J, Silipo A, Molinaro A. "Rules of Engagement" of Protein-Glycoconjugate Interactions: A Molecular View Achievable by using NMR Spectroscopy and Molecular Modeling. ChemistryOpen 2016; 5:274-96. [PMID: 27547635 PMCID: PMC4981046 DOI: 10.1002/open.201600024] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Indexed: 12/20/2022] Open
Abstract
Understanding the dynamics of protein-ligand interactions, which lie at the heart of host-pathogen recognition, represents a crucial step to clarify the molecular determinants implicated in binding events, as well as to optimize the design of new molecules with therapeutic aims. Over the last decade, advances in complementary biophysical and spectroscopic methods permitted us to deeply dissect the fine structural details of biologically relevant molecular recognition processes with high resolution. This Review focuses on the development and use of modern nuclear magnetic resonance (NMR) techniques to dissect binding events. These spectroscopic methods, complementing X-ray crystallography and molecular modeling methodologies, will be taken into account as indispensable tools to provide a complete picture of protein-glycoconjugate binding mechanisms related to biomedicine applications against infectious diseases.
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Affiliation(s)
- Roberta Marchetti
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
| | - Serge Perez
- Department Molecular Pharmacochemistry UMR 5063CNRS and University of GrenobleAlpes, BP 5338041 Grenoble cedex 9France
| | - Ana Arda
- Bizkaia Technological ParkCIC bioGUNEBuilding 801A-148160Derio-BizkaiaSpain
| | - Anne Imberty
- Centre de Recherche sur les CNRSand University of Grenoble Macromolécules Végétales, UPR 5301Alpes, BP 5338041Grenoble cedex 9France
| | | | - Alba Silipo
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
| | - Antonio Molinaro
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
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16
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Antanasijevic A, Kingsley C, Basu A, Bowlin TL, Rong L, Caffrey M. Application of virus-like particles (VLP) to NMR characterization of viral membrane protein interactions. JOURNAL OF BIOMOLECULAR NMR 2016; 64:255-65. [PMID: 26921030 PMCID: PMC4826305 DOI: 10.1007/s10858-016-0025-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 02/22/2016] [Indexed: 05/10/2023]
Abstract
The membrane proteins of viruses play critical roles in the virus life cycle and are attractive targets for therapeutic intervention. Virus-like particles (VLP) present the possibility to study the biochemical and biophysical properties of viral membrane proteins in their native environment. Specifically, the VLP constructs contain the entire protein sequence and are comprised of native membrane components including lipids, cholesterol, carbohydrates and cellular proteins. In this study we prepare VLP containing full-length hemagglutinin (HA) or neuraminidase (NA) from influenza and characterize their interactions with small molecule inhibitors. Using HA-VLP, we first show that VLP samples prepared using the standard sucrose gradient purification scheme contain significant amounts of serum proteins, which exhibit high potential for non-specific interactions, thereby complicating NMR studies of ligand-target interactions. We then show that the serum contaminants may be largely removed with the addition of a gel filtration chromatography step. Next, using HA-VLP we demonstrate that WaterLOGSY NMR is significantly more sensitive than Saturation Transfer Difference (STD) NMR for the study of ligand interactions with membrane bound targets. In addition, we compare the ligand orientation to HA embedded in VLP with that of recombinant HA by STD NMR. In a subsequent step, using NA-VLP we characterize the kinetic and binding properties of substrate analogs and inhibitors of NA, including study of the H274Y-NA mutant, which leads to wide spread resistance to current influenza antivirals. In summary, our work suggests that VLP have high potential to become standard tools in biochemical and biophysical studies of viral membrane proteins, particularly when VLP are highly purified and combined with control VLP containing native membrane proteins.
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Affiliation(s)
- Aleksandar Antanasijevic
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S Ashland, Chicago, IL, 60607, USA
| | - Carolyn Kingsley
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S Ashland, Chicago, IL, 60607, USA
| | - Arnab Basu
- Microbiotix Inc., Worcester, MA, 01605, USA
| | | | - Lijun Rong
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Michael Caffrey
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S Ashland, Chicago, IL, 60607, USA.
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17
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Sharmila DJS, Jino Blessy J. Molecular dynamics of sialic acid analogues complex with cholera toxin and DFT optimization of ethylene glycol-mediated zinc nanocluster conjugation. J Biomol Struct Dyn 2016; 35:182-206. [PMID: 26733187 DOI: 10.1080/07391102.2015.1136689] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Cholera is an infectious disease caused by cholera toxin (CT) protein of bacterium Vibrio cholerae. A sequence of sialic acid (N-acetylneuraminic acid, NeuNAc or Neu5Ac) analogues modified in its C-5 position is modelled using molecular modelling techniques and docked against the CT followed by molecular dynamics simulations. Docking results suggest better binding affinity of NeuNAc analogue towards the binding site of CT. The NeuNAc analogues interact with the active site residues GLU:11, TYR:12, HIS:13, GLY:33, LYS:34, GLU:51, GLN:56, HIE:57, ILE:58, GLN:61, TRP:88, ASN:90 and LYS:91 through intermolecular hydrogen bonding. Analogues N-glycolyl-NeuNAc, N-Pentanoyl-NeuNAc and N-Propanoyl-NeuNAc show the least XPGscore (docking score) of -9.90, -9.16, and -8.91, respectively, and glide energy of -45.99, -42.14 and -41.66 kcal/mol, respectively. Stable nature of CT-N-glycolyl-NeuNAc, CT-N-Pentanoyl-NeuNAc and CT-N-Propanoyl-NeuNAc complexes was verified through molecular dynamics simulations, each for 40 ns using the software Desmond. All the nine NeuNAc analogues show better score for drug-like properties, so could be considered as suitable candidates for drug development for cholera infection. To improve the enhanced binding mode of NeuNAc analogues towards CT, the nine NeuNAc analogues are conjugated with Zn nanoclusters through ethylene glycol (EG) as carriers. The NeuNAc analogues conjugated with EG-Zn nanoclusters show better binding energy towards CT than the unconjugated nine NeuNAc analogues. The electronic structural optimization of EG-Zn nanoclusters was carried out for optimizing their performance as better delivery vehicles for NeuNAc analogues through density functional theory calculations. These sialic acid analogues may be considered as novel leads for the design of drug against cholera and the EG-Zn nanocluster may be a suitable carrier for sialic acid analogues.
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Affiliation(s)
- D Jeya Sundara Sharmila
- a Department of Nano Science and Technology , Tamil Nadu Agricultural University , Coimbatore 641003 , Tamil Nadu , India
| | - J Jino Blessy
- b Department of Bioinformatics , Karunya University , Karunya Nagar, Coimbatore 641 114 , Tamil Nadu , India
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18
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Kannan S, Kolandaivel P. Computational studies of pandemic 1918 and 2009 H1N1 hemagglutinins bound to avian and human receptor analogs. J Biomol Struct Dyn 2015; 34:272-89. [PMID: 25893548 DOI: 10.1080/07391102.2015.1027737] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The purpose of this work was to study the binding properties of two pandemic influenza A virus 1918 H1N1 (SC1918) and 2009 H1N1 (CA09) hemagglutinin (HA) with avian and human receptors. The quantum chemical calculations have been performed to analyze the interactions of 130 loop, 190 helix, 220 loop region, and conserved residues 95,145,153-155, of pandemic viruses' HA with sialo-trisaccharide receptor of avian and human using density functional theory. The HA's residues Tyr 95, Ala 138, Gln 191, Arg 220, and Asp 225 from the above regions have stronger interaction with avian receptor. The residues Thr 136, Trp 153, His 183, and Asp 190 of HA are important and play a significant role to bind with human receptor. The residues Tyr 95, Ala 138, Lys 145, Trp 153, Gln 192, and Gln 226 of HA of CA09 virus have found more interaction energies with human than avian receptors. Due to mutations in the active residues of HA of CA09 virus comparing with SC1918, the binding capabilities of HA with human have been increased. The molecular dynamics simulation was made to understand the different dynamical properties of HA and molecular interactions between HA of these two viruses with sialo-trisaccharide receptors of avian and human receptors. The interaction energy of HA of CA09 virus with human receptor decreases due to the human receptor far away from conserved residue region of HA protein. This reveals that the conserved residues particularly Lys 145 play major contribution to interaction with human receptor in HA of CA09 virus.
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Affiliation(s)
- S Kannan
- a Department of Physics , Bharathiar University , Coimbatore 641 046 , India
| | - P Kolandaivel
- a Department of Physics , Bharathiar University , Coimbatore 641 046 , India
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19
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Marchetti R, Molinaro A, Silipo A. NMR as a Tool to Unveil the Molecular Basis of Glycan-mediated Host–Pathogen Interactions. CARBOHYDRATES IN DRUG DESIGN AND DISCOVERY 2015. [DOI: 10.1039/9781849739993-00021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The nature of the relationship between microbes and hosts spans the broad spectrum from beneficial (symbiosis) to pathogenic (disease); one of the key factors determining the establishment of any type of host–microbe interaction is the pattern of glycoconjugates exposed on cell surfaces, many known as virulence factors since they are pivotal for adhesion to host tissue, immunoevasion and immunosuppression, causing disease in the host. The recognition of these pathogen glycostructures by specific host receptors is an important means of immune defense. In this context, NMR represents a valuable tool to investigate the conformational properties of both host/pathogen signaling molecules and to disclose their interaction at a molecular level. This chapter provides an overview of several protein–carbohydrate interaction systems studied by NMR, and their implications in human and plant diseases.
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Affiliation(s)
- Roberta Marchetti
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant’Angelo Via Cintia 4 I-80126 Napoli Italy
| | - Antonio Molinaro
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant’Angelo Via Cintia 4 I-80126 Napoli Italy
| | - Alba Silipo
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant’Angelo Via Cintia 4 I-80126 Napoli Italy
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20
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Ardá A, Canales A, Cañada FJ, Jiménez-Barbero J. Carbohydrate–Protein Interactions: A 3D View by NMR. CARBOHYDRATES IN DRUG DESIGN AND DISCOVERY 2015. [DOI: 10.1039/9781849739993-00001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
NMR spectroscopy is a key tool for carbohydrate research. In studies with complex oligosaccharides there are limits to the amount of relevant structural information provided by these observables due to problems of signal overlapping, strong coupling and/or the scarcity of the key NOE information. Thus, there is an increasing need for additional parameters with structural information, such as residual dipolar couplings (RDCs), paramagnetic relaxation enhancements (PREs) or pseudo contact shifts (PCSs). Carbohydrates are rather flexible molecules. Therefore, NMR observables do not always correlate with a single conformer but with an ensemble of low free-energy conformers that can be accessed by thermal fluctuations. Depending on the system under study, different NMR approaches can be followed to characterize protein–carbohydrate interactions: the standard methodologies can usually be classified as “ligand-based” or “receptor-based”. The selection of the proper methodology is usually determined by the size of the receptor, the dissociation constant of the complex (KD), the availability of the labelled protein (15N, 13C) and the access to soluble receptors at enough concentration for NMR measurements.
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Affiliation(s)
- Ana Ardá
- Chemical and Physical Biology, CIB-CSIC Ramiro de Maeztu 9 28040 Madrid Spain
| | - Angeles Canales
- Chemical and Physical Biology, CIB-CSIC Ramiro de Maeztu 9 28040 Madrid Spain
| | - F. Javier Cañada
- Chemical and Physical Biology, CIB-CSIC Ramiro de Maeztu 9 28040 Madrid Spain
| | - Jesús Jiménez-Barbero
- Chemical and Physical Biology, CIB-CSIC Ramiro de Maeztu 9 28040 Madrid Spain
- CIC bioGUNE, Parque Tecnológico de Bizkaia Edif. 801A-1 48160 Derio-Bizkaia Spain
- Ikerbasque, Basque Foundation for Science Bilbao Spain
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21
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Blessy JJ, Sharmila DJS. Molecular modeling of methyl-α-Neu5Ac analogues docked against cholera toxin - a molecular dynamics study. Glycoconj J 2015; 32:49-67. [DOI: 10.1007/s10719-014-9570-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 11/26/2014] [Accepted: 11/27/2014] [Indexed: 10/24/2022]
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22
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Abstract
NMR has proven to be an invaluable technique for identifying and characterizing ligand interactions with biomolecules. NMR-based detection of ligand binding to protein targets is described. Specifically, the use of the WaterLOGSY NMR experiment to screen mixtures of compounds from a fragment library for binding to influenza H5 hemagglutinin is detailed.
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Affiliation(s)
- Benjamin E Ramirez
- Center for Structural Biology, University of Illinois at Chicago, 1100 S. Ashland Ave, Chicago, IL, 60607, USA
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23
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Antanasijevic A, Ramirez B, Caffrey M. Comparison of the sensitivities of WaterLOGSY and saturation transfer difference NMR experiments. JOURNAL OF BIOMOLECULAR NMR 2014; 60:37-44. [PMID: 25015532 PMCID: PMC4201884 DOI: 10.1007/s10858-014-9848-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 07/08/2014] [Indexed: 05/15/2023]
Abstract
The WaterLOGSY (WL) and saturation transfer difference (STD) NMR experiments have proven to be extremely useful techniques to characterize interactions between small molecules and large biomolecules. In this work we compare the relative sensitivities of WL and STD NMR using 3 experimental systems: ketoprofen (KET)-bovine serum albumin (BSA), tert-butyl hydroquinone (TBHQ)-hemagglutinin (HA), and chloramphenicol (CAM)-ribosome (70S). In all cases we find that WL is more sensitive than STD for a given experimental time with the ratios ranging from 3.2 for KET-BSA to 16 for TBHQ-HA and CAM-70S. We attribute the increased sensitivity of WL to be due to simultaneous saturation of multiple sources of cross correlation, including direct NOEs of 1H of water and exchangeable groups and indirect NOEs of 1H-C groups. We suggest that the outstanding sensitivity of WL make it ideally suited for drug screening efforts targeting very large biomolecules at relatively low concentrations.
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Affiliation(s)
- Aleksandar Antanasijevic
- Department of Biochemistry & Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607 USA
| | - Benjamin Ramirez
- Department of Biochemistry & Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607 USA
| | - Michael Caffrey
- Department of Biochemistry & Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607 USA
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24
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Lao YH, Chiang HY, Yang DK, Peck K, Chen LC. Selection of aptamers targeting the sialic acid receptor of hemagglutinin by epitope-specific SELEX. Chem Commun (Camb) 2014; 50:8719-22. [PMID: 24964092 DOI: 10.1039/c4cc03116d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new SELEX scheme is proposed for the selection of aptamers targeting a specific epitope of a native protein. Anti-sialic acid receptor (SAR) aptamers that inhibit H1 hemagglutination at a low picomole dose are selected accordingly.
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Affiliation(s)
- Yeh-Hsing Lao
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan.
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25
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Ratia K, Light SH, Antanasijevic A, Anderson WF, Caffrey M, Lavie A. Discovery of selective inhibitors of the Clostridium difficile dehydroquinate dehydratase. PLoS One 2014; 9:e89356. [PMID: 24586713 PMCID: PMC3931744 DOI: 10.1371/journal.pone.0089356] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 01/18/2014] [Indexed: 12/18/2022] Open
Abstract
A vibrant and healthy gut flora is essential for preventing the proliferation of Clostridium difficile, a pathogenic bacterium that causes severe gastrointestinal symptoms. In fact, most C. difficile infections (CDIs) occur after broad-spectrum antibiotic treatment, which, by eradicating the commensal gut bacteria, allows its spores to proliferate. Hence, a C. difficile specific antibiotic that spares the gut flora would be highly beneficial in treating CDI. Towards this goal, we set out to discover small molecule inhibitors of the C. difficile enzyme dehydroquinate dehydratase (DHQD). DHQD is the 3(rd) of seven enzymes that compose the shikimate pathway, a metabolic pathway absent in humans, and is present in bacteria as two phylogenetically and mechanistically distinct types. Using a high-throughput screen we identified three compounds that inhibited the type I C. difficile DHQD but not the type II DHQD from Bacteroides thetaiotaomicron, a highly represented commensal gut bacterial species. Kinetic analysis revealed that the compounds inhibit the C. difficile enzyme with Ki values ranging from 10 to 20 µM. Unexpectedly, kinetic and biophysical studies demonstrate that inhibitors also exhibit selectivity between type I DHQDs, inhibiting the C. difficile but not the highly homologous Salmonella enterica DHQD. Therefore, the three identified compounds seem to be promising lead compounds for the development of C. difficile specific antibiotics.
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Affiliation(s)
- Kiira Ratia
- Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Samuel H. Light
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Aleksandar Antanasijevic
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Wayne F. Anderson
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Michael Caffrey
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Arnon Lavie
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
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26
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New small molecule entry inhibitors targeting hemagglutinin-mediated influenza a virus fusion. J Virol 2013; 88:1447-60. [PMID: 24198411 DOI: 10.1128/jvi.01225-13] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Influenza viruses are a major public health threat worldwide, and options for antiviral therapy are limited by the emergence of drug-resistant virus strains. The influenza virus glycoprotein hemagglutinin (HA) plays critical roles in the early stage of virus infection, including receptor binding and membrane fusion, making it a potential target for the development of anti-influenza drugs. Using pseudotype virus-based high-throughput screens, we have identified several new small molecules capable of inhibiting influenza virus entry. We prioritized two novel inhibitors, MBX2329 and MBX2546, with aminoalkyl phenol ether and sulfonamide scaffolds, respectively, that specifically inhibit HA-mediated viral entry. The two compounds (i) are potent (50% inhibitory concentration [IC50] of 0.3 to 5.9 μM); (ii) are selective (50% cytotoxicity concentration [CC(50)] of >100 μM), with selectivity index (SI) values of >20 to 200 for different influenza virus strains; (iii) inhibit a wide spectrum of influenza A viruses, which includes the 2009 pandemic influenza virus A/H1N1/2009, highly pathogenic avian influenza (HPAI) virus A/H5N1, and oseltamivir-resistant A/H1N1 strains; (iv) exhibit large volumes of synergy with oseltamivir (36 and 331 μM(2) % at 95% confidence); and (v) have chemically tractable structures. Mechanism-of-action studies suggest that both MBX2329 and MBX2546 bind to HA in a nonoverlapping manner. Additional results from HA-mediated hemolysis of chicken red blood cells (cRBCs), competition assays with monoclonal antibody (MAb) C179, and mutational analysis suggest that the compounds bind in the stem region of the HA trimer and inhibit HA-mediated fusion. Therefore, MBX2329 and MBX2546 represent new starting points for chemical optimization and have the potential to provide valuable future therapeutic options and research tools to study the HA-mediated entry process.
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Mair CM, Ludwig K, Herrmann A, Sieben C. Receptor binding and pH stability - how influenza A virus hemagglutinin affects host-specific virus infection. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:1153-68. [PMID: 24161712 DOI: 10.1016/j.bbamem.2013.10.004] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 09/26/2013] [Accepted: 10/01/2013] [Indexed: 11/28/2022]
Abstract
Influenza A virus strains adopt different host specificities mainly depending on their hemagglutinin (HA) protein. Via HA, the virus binds sialic acid receptors of the host cell and, upon endocytic uptake, HA triggers fusion between the viral envelope bilayer and the endosomal membrane by a low pH-induced conformational change leading to the release of the viral genome into the host cell cytoplasm. Both functions are crucial for viral infection enabling the genesis of new progeny virus. Adaptation to different hosts in vitro was shown to require mutations within HA altering the receptor binding and/or fusion behavior of the respective virus strain. Human adapted influenza virus strains (H1N1, H3N2, H2N2) as well as recent avian influenza virus strains (H5, H7 and H9 subtypes) which gained the ability to infect humans mostly contained mutations in the receptor binding site (RBS) of HA enabling increased binding affinity of these viruses to human type (α-2,6 linked sialic acid) receptors. Thus, the receptor binding specificity seems to be the major requirement for successful adaptation to the human host; however, the RBS is not the only determinant of host specificity. Increased binding to a certain cell type does not always correlate with infection efficiency. Furthermore, viruses carrying mutations in the RBS often resulted in reduced viral fitness and were still unable to transmit between mammals. Recently, the pH stability of HA was reported to affect the transmissibility of influenza viruses. This review summarizes recent findings on the adaptation of influenza A viruses to the human host and related amino acid substitutions resulting in altered receptor binding specificity and/or modulated fusion pH of HA. Furthermore, the role of these properties (receptor specificity and pH stability of HA) for adaptation to and transmissibility in the human host is discussed. This article is part of a Special Issue entitled: Viral Membrane Proteins -- Channels for Cellular Networking.
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Affiliation(s)
- Caroline M Mair
- Group of Molecular Biophysics, Institute of Biology, Humboldt University Berlin, Invalidenstraße 42, 10115 Berlin, Germany
| | - Kai Ludwig
- Research center of Electron Microscopy, Institute of Chemistry and Biochemistry, Free University Berlin, Fabeckstraße 36a, 14195 Berlin, Germany
| | - Andreas Herrmann
- Group of Molecular Biophysics, Institute of Biology, Humboldt University Berlin, Invalidenstraße 42, 10115 Berlin, Germany.
| | - Christian Sieben
- Group of Molecular Biophysics, Institute of Biology, Humboldt University Berlin, Invalidenstraße 42, 10115 Berlin, Germany
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Antanasijevic A, Cheng H, Wardrop DJ, Rong L, Caffrey M. Inhibition of influenza H7 hemagglutinin-mediated entry. PLoS One 2013; 8:e76363. [PMID: 24194835 PMCID: PMC3806803 DOI: 10.1371/journal.pone.0076363] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 08/26/2013] [Indexed: 12/20/2022] Open
Abstract
The recent outbreak of H7N9 influenza in China is of high concern to public health. H7 hemagglutinin (HA) plays a critical role in influenza entry and thus HA presents an attractive target for antivirals. Previous studies have suggested that the small molecule tert-butyl hydroquinone (TBHQ) inhibits the entry of influenza H3 HA by binding to the stem loop of HA and stabilizing the neutral pH conformation of HA, thereby disrupting the membrane fusion step. Based on amino acid sequence, structure and immunogenicity, H7 is a related Group 2 HA. In this work we show, using a pseudovirus entry assay, that TBHQ inhibits H7 HA-mediated entry, as well as H3 HA-mediated entry, with an IC50 ~ 6 µM. Using NMR, we show that TBHQ binds to the H7 stem loop region. STD NMR experiments indicate that the aromatic ring of TBHQ makes extensive contact with the H7 HA surface. Limited proteolysis experiments indicate that TBHQ inhibits influenza entry by stabilizing the H7 HA neutral pH conformation. Together, this work suggests that the stem loop region of H7 HA is an attractive target for therapeutic intervention and that TBHQ, which is a widely used food preservative, is a promising lead compound.
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Affiliation(s)
- Aleksandar Antanasijevic
- Department of Biochemistry & Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Han Cheng
- Department of Microbiology & Immunology, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Duncan J. Wardrop
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Lijun Rong
- Department of Microbiology & Immunology, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Michael Caffrey
- Department of Biochemistry & Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
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Choi YH, Kim JH, Park JH, Lee N, Kim DH, Jang KS, Park ILH, Kim BG. Protein engineering of α2,3/2,6-sialyltransferase to improve the yield and productivity of in vitro sialyllactose synthesis. Glycobiology 2013; 24:159-69. [DOI: 10.1093/glycob/cwt092] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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Effect of oseltamivir carboxylate consumption on emergence of drug-resistant H5N2 avian influenza virus in Mallard ducks. Antimicrob Agents Chemother 2013; 57:2171-81. [PMID: 23459475 DOI: 10.1128/aac.02126-12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Oseltamivir carboxylate (OC) has been detected in environmental waters at various levels during recent influenza seasons in humans, reflecting levels of usage and stability of this drug. In consideration of the role of waterfowl as hosts for influenza viruses that may contribute to human infections, we evaluated the effect of consumption of low doses of OC on development of oseltamivir-resistant influenza virus mutants in mallard ducks (Anas platyrhynchos) infected with two different low-pathogenic (LP) H5N2 avian influenza viruses (AIV). We detected development of virus variants carrying a known molecular marker of oseltamivir resistance (neuraminidase E119V) in 4 out of 6 mallards infected with A/Mallard/Minnesota/182742/1998 (H5N2) and exposed to 1,000 ng/liter OC. The mutation first appeared as a minor population on days 5 to 6 and was the dominant genotype on days 6 to 8. Oseltamivir-resistant mutations were not detected in virus from ducks not exposed to the drug or in ducks infected with a second strain of virus and similarly exposed to OC. Virus isolates carrying the E119V mutation displayed in vitro replication kinetics similar to those of the wild-type virus, but in vivo, the E119V virus rapidly reverted back to wild type in the absence of OC, and only the wild-type parental strain was transmitted to contact ducks. These results indicate that consumption by wild waterfowl of OC in drinking water may promote selection of the E119V resistance mutation in some strains of H5N2 AIV that could contribute to viruses infecting human populations.
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Simčič M, Sosič I, Hodošček M, Barreteau H, Blanot D, Gobec S, Grdadolnik SG. The binding mode of second-generation sulfonamide inhibitors of MurD: clues for rational design of potent MurD inhibitors. PLoS One 2012; 7:e52817. [PMID: 23285193 PMCID: PMC3527612 DOI: 10.1371/journal.pone.0052817] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 11/23/2012] [Indexed: 11/19/2022] Open
Abstract
A series of optimized sulfonamide derivatives was recently reported as novel inhibitors of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (MurD). These are based on naphthalene-N-sulfonyl-D-glutamic acid and have the D-glutamic acid replaced with rigidified mimetics. Here we have defined the binding site of these novel ligands to MurD using (1)H/(13)C heteronuclear single quantum correlation. The MurD protein was selectively (13)C-labeled on the methyl groups of Ile (δ1 only), Leu and Val, and was isolated and purified. Crucial Ile, Leu and Val methyl groups in the vicinity of the ligand binding site were identified by comparison of chemical shift perturbation patterns among the ligands with various structural elements and known binding modes. The conformational and dynamic properties of the bound ligands and their binding interactions were examined using the transferred nuclear Overhauser effect and saturation transfer difference. In addition, the binding mode of these novel inhibitors was thoroughly examined using unrestrained molecular dynamics simulations. Our results reveal the complex dynamic behavior of ligand-MurD complexes and its influence on ligand-enzyme contacts. We further present important findings for the rational design of potent Mur ligase inhibitors.
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Affiliation(s)
- Mihael Simčič
- EN-FIST Centre of Excellence, Ljubljana, Slovenia
- Laboratory of Biomolecular Structure, National Institute of Chemistry, Ljubljana, Slovenia
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Milan Hodošček
- Laboratory of Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia
| | - Hélène Barreteau
- Laboratoire des Enveloppes Bactériennes et Antibiotiques, Université Paris-Sud, Orsay, France
| | - Didier Blanot
- Laboratoire des Enveloppes Bactériennes et Antibiotiques, Université Paris-Sud, Orsay, France
- Centre National de la Recherche Scientifique, Orsay, France
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Simona Golič Grdadolnik
- EN-FIST Centre of Excellence, Ljubljana, Slovenia
- Laboratory of Biomolecular Structure, National Institute of Chemistry, Ljubljana, Slovenia
- * E-mail:
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